I managed to get all of them over the course of the game using the following videos as a visual guide. Special thanks to IXNITE for making and posting these videos; he gets ALL the credit. Not me.

Note: Some of the Flags and Spy-Ops, it is highly recommended you use a sniper rifle weapon to get these as you need to shoot the Spy-Ops and Flags to collect them, and as indicated in the videos below, they can be placed at very far distances.

Edit: Regarding the note above about using sniper rifles for shooting Flags and Spy-Ops, using normal guns will not work - their bullets will not reach these targets, so stick to sniper rifles. Thanks to MushaConvoy for pointing this out.

Edit: If you're having trouble getting Mysterious Letter "N" in Chapter 2 (Look at 3:35 of the video on Chapter 2), I suggest that, when you activate the raised platforms, stay to the left when you enter - do NOT go down the middle otherwise you will trigger the Boss Fight AFTER you complete the boss fight, go back to the control panel and activate it again. Thanks again to MushaConvoy and Wanderer128 for pointing this trouble spot out

Hope this helps.

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